Metagenomic analysis reveals hidden links between gut microbes and habitat adaptation among cave and surface dwelling Sinocyclocheilus species

Intestinal microbes are closely related to vital host functions such as digestion and nutrient absorption,which play important roles in enhancing host adaptability.As a natural“laboratory”,caves provide an outstanding model for understanding the significance of gut microbes and feeding habits in the habitat adaptability of hosts.However,research on the relationship between gut microbes,feeding habits,and the adaptability of troglobites remains insufficient.In this study,we compared the characteristics of the intestinal microbes of Sinocyclocheilus cavefish and surface fish and further established the relationship between intestinal and habitat microbes.Furthermore,we conducted environmental DNA(eDNA)(metabarcoding)analysis of environmental samples to clarify the composition of potential food resources in the habitats of the Sinocyclocheilus cavefish and surface fish.Results showed that the structure of the Sinocyclocheilus gut microbes was more related to ecological type(habitat type)than phylogenetic relationships.While horizontal transfer of habitat microbes was a source of gut microbes,hosts also showed strong selection for inherent microbes as dominant microorganisms.Differences in the composition and structure of gut microbes,especially dominant microbes,may enhance the adaptability of the two Sinocyclocheilus fish types from the perspectives of food intake,nutrient utilization,and harmful substance metabolism,suggesting that food resources,predation patterns,intestinal flora,digestive and absorptive capacity,and feeding habits and preferences are linked to habitat adaptability.These results should facilitate our understanding of the significance of fish gut microbes to habitat adaptation and provide a new perspective for studying the adaptive mechanisms of cavefish.

Effects of foraging site distances on the intestinal bacterial community compositions of the sympatric wintering Hooded Crane(Grus monacha)and Domestic Duck(Anas platyrhynchos domesticus)

Background:The composition of intestinal microflora in animals is affected by cross-species transmission.In a nature reserve,the foraging sites of waterbirds are relatively fixed,but frequently close to residential areas and can also be visited by domestic fowls.It is easy to result in the trans-species-flock dispersal of gut microbes between the wild birds and domestic fowls.The effects of the variable foraging site distances on the gut microbe structures of the waterbirds and the sympatric domestic fowls are currently unclear,and further research is required to evaluate the impacts of geographic location on cross-infection.Methods:Illumina high-throughput sequencing and bioinformatics analysis software were utilized to compare and analyze the composition of gut microbes from the fecal samples of Hooded Cranes(HC;Grus monacha)and two groups of Domestic Ducks(Anas platyrhynchos domesticus)that foraged at 1 km(ducks in near areas,D-N),and 4 km(ducks in far areas,D-F)away from the habitats of the Hooded Cranes at Shengjin Lake,China.Results:The results showed that there were significant differences in the alpha-diversity of the gut bacteria in the HC,D-N,and D-F samples under the interspecific distance factor.The dominant bacterial phyla,Cyanobacteria and Proteobacteria,showed correlations with distance for each host.The D-N group had more diverse intestinal flora than the D-F,as they were physically closer to the HC and had more indirect contact and cross-transmission of their gut microbes.More potentially pathogenic bacterial sequences,and Operational Taxonomic Units(OTUs)were found in the D-N than in HC and D-F.Conclusions:Hooded Cranes and the Domestic Duck populations at variable distances from the cranes showed significant differences in their intestinal bacteria and potentially pathogenic bacteria.The closer the foraging sites were,the easier the intestinal flora spread across species.The results provide a basis for determining the safe distance between wild birds and domestic fowls in a nature reserve.

Research Progress on the Relationship between Intestinal Flora and Mental and Psychological Diseases

The effects of microorganisms on the central nervous system are manifested in both health and disease states. The symbiotic microorganisms in the human gut have certain effects on the brain development before and after birth. Chronic inflammation in patients with irritable bowel syndrome (IBS), psychiatric disorders such as PTSD, anxiety disorders, etc., is likely to be associated with an imbalance in gut flora. Intestinal flora regulates the central nervous system mainly through nerve, endocrine, metabolic and immune pathways. The mechanisms involved in the influence of intestinal flora on the central nervous system are diverse, so it is necessary to explore the role of intestinal flora in mental and psychological diseases.

Large intestinal dynamics differ between fowl and swine:Anatomical modifications,microbial collaboration,and digestive advantages from fibrolytic enzymes

The large intestinal systems of fowl and swine recover nutrients from ileal indigesta by a strategically different manner.Indigesta with fowl enter a short colon where retro-peristalsis using urine from the urodeum carries small particulates and solutes into both ceca while coarse materials collect in the cloaca.Fowl repetitively add fine and soluble materials into both ceca to continue fermentation until complexity of the remainder exceeds microbial action,then contents apart from faeces are entirely evacuated.Indigesta with swine initially enter a short cecum followed by a lengthy progression through to the rectal ampulla.Wall out-pocketings of circular muscle or haustrae occur throughout the length of the pig's cecum and helicoidal colon.Each pocket carries contents acquired earlier in the cecum.Motility collects fines and solutes into haustrae during their progression through the colon whereas coarse particulates assemble in the core.Haustrae contents continually ferment during movement to the distal colon with resulting volatile fatty acids(VFA)and electrolytes being absorbed.Mucin loosely covers the lumen surface in caeca as well as helicoidal colon that may capture microbes from active intestinal contents as well as release others to sustain fermentation.The microbial community continually modifies to accommodate fibre complexity as encountered.Resistant starches(RS)and simple oligosaccharides rapidly ferment to yield VFA while encouraging butyric acid in the cecum and anterior colon,whereas non-starch polysaccharides(NSP)complexity requires extended durations through the remaining colon that enhance acetic acid.Residual fibre eventually results in undue complexity for fermentation and consolidates at termination of the colon.These compact pellets are placed on core contents to form faeces having a nodular surface.Acetic,propionic,and butyric acids represent the bulk of VFA and are derived from non-digestible carbohydrates.Fibrolytic enzymes,when supplemented to feed,may increase the proportion of oligosaccharides and simpler NSP to further the rate as well as extent of fermentation.Active absorption of VFA by mucosal enterocytes employs its ionized form together with Na^(+),whereas direct membrane passage occurs when non-dissociated.Most absorbed VFA favour use by the host with a portion of butyric acid together with by-products from protein digestion being retained to reform mucin and sustain mucosal integrity.

Pathogenesis of autoimmune hepatitis

Autoimmune hepatitis(AIH)is a chronic progressive liver disease whose etiology and pathogenesis are not yet clear.It is currently believed that the occurrence of AIH is closely related to genetic susceptibility and immune abnormalities,and other factors such as environment,viral infection and drugs that may cause immune dysfunction.This article reviews the pathogenesis of AIH and describes the latest research results in the past 5 years.

Role of dietary amino acids and microbial metabolites in the regulation of pig intestinal health

With the rapid development of sequencing technology,research on pigs has focused on intestinal microbes.Accumulating evidence suggests that the metabolites of intestinal microbes are the key medium for interactions between microbes and the host.Amino acid metabolism is involved in the growth and immune processes of pigs.The gut microbes of pigs are heavily involved in the metabolism of amino acids in their hosts.Here,we review the latest relevant literature.Research findings show that microbial metabolites,such as indoles,short-chain fatty acids,and ammonia,play a key role in gut health.Moreover,we summarize the effects of amino acids on the structure of the gut microbial community and the metabolism of amino acids by pig gut microbes.Evidence shows that microbial amino acid metabolites act as signal molecules in the intestine and play an important role in the intestinal health of pigs.

Gut fungal community and its probiotic effect on Bactrocera dorsalis

The oriental fruit fly,Bactrocera dorsalis(Diptera:Tephritidae)is a destructive horticultural pest which causes considerable economic losses every year.A collection of microorganisms live within the B.dorsalis gut,and they are involved in its development,physiology,and behavior.However,knowledge regarding the composition and function of the gut mycobiota in B.dorsalis are still limited.Here,we comprehensively characterized the gut mycobiota in B.dorsalis across different developmental stages.High-throughput sequencing results showed a significant difference in fungal species abundance and diversity among different developmental stages of B.dorsalis.Quantitative polymerase chain reaction and culture-dependent methods showed that yeast species was the dominant group in the larval stage.We isolated 13 strains of yeast from the larval gut,and found that GF(germ-free)larvae mono-associated with strain Hanseniaspora uvarum developed faster than those mono-associated with other tested fungal strains.Supplementing the larval diet with H.uvarum fully rescued B.dorsalis development,shortened the larval developmental time,and increased adult wing lengths,as well as the body sizes and weights of both pupae and adults.Thus,our study highlights the close interactions between gut fungi,especially H.uvarum,and B.dorsalis.These findings can be applied to the sterile insect technique program to promote host development during mass insect rearing.

Effects of biological flocculation technology(BFT)on water quality dynamics and immune response of grass carp(Ctenopharyngodon idella)

The biofloc technology(BFT)offers benefits in improving feed utilization and reducing the feed conversion ratio compared to the recirculating aquaculture system(RAS).In this study,high-throughput 16S rRNA gene sequencing was employed to investigate and compare the bacterial communities in these aquaculture systems and the gut microbiota of grass carp reared in them.We observed a significant distinction between the microbial communities of the aquaculture systems and the intestinal microbiota of grass carp.The genera cetobacterium and bacillus were more abundant in the BFT system,accounting for only 0.05% and 0.25% in the RAS.Our study also demonstrated that BFT could influence the intestinal microorganisms of grass carp(Ctenopharyngodon Idella)by reducing the relative abundance of burkholderia-caballeronia-paraburkholderia and increasing that of cetobacterium.Based on bugBase community predictions,the potential pathogenicity in BFT and grass carp intestine was lower than in RAS.Regarding gene expression in the grass carp intestine,immunosuppressive genes showed higher expression,while pro-inflammatory genes exhibited lower expression in grass carp reared in BFT.Furthermore,the final average length and weight of grass carp in the BFT system were significantly higher than those in the RAS.This study provides valuable insights into gut microbiome ecology in relation to two grass carp aquaculture systems,which could be effectively applied in grass carp management to promote health and improve water quality.